Guy Cochrane < People & groups < About us < EMBL-EBI

Guy Cochrane

Guy Cochrane

Team Leader - Cochrane team: European Nucleotide Archive

PhD University of East Anglia, 1999. At EMBL-EBI since 2002, Team leader since 2009.

cochrane [at] ebi.ac.uk

Tel:+44 (0)1223 492 564 / Fax:+44 (0)1223 494 468

Cochrane team

The European Nucleotide Archive (ENA) team, led by Dr Guy Cochrane, provides globally comprehensive primary data repositories for nucleotide sequencing information. ENA content spans the spectrum of data: from raw sequence reads through assembly to functional annotation of assembled sequences and genomes. The team provides interactive and programmatic submission tools as well as curation support.

The ENA offers a broad palette of services over the web, via a powerful programmatic interface. All ENA services are supported with a helpdesk and training programme. Reflecting the centrality of nucleotide sequencing in the life sciences and the emerging importance of the technologies in applied areas such as healthcare, environmental and food sciences, ENA data and services form a core foundation upon which scientific understanding of biological systems has been assembled. With ongoing focus on data presentation, integration within ENA, integration with resources external to ENA, tools provision and services development, the team’s commitment is to the utility of ENA content and achieving the broadest reach of sequencing applications.

In addition to the ENA resource itself, the team also provides core sequence archiving technology, content and services that are used in the construction and delivery of many other EBI resources, including the European Genome-phenome Archive, the Metagenomics Portal, ArrayExpress and the UniProt Knowledgebase.

Publications

2013

The International Nucleotide Sequence Database Collaboration

Nakamura, Y., Cochrane G., Karsch-mizrachi I., and on behalf of the Collaboration International Nucleotide Sequence Database

Nucleic Acids Res. Volume 41, Number D1, (2013), p.D21-D24 doi:

Facing growth in the European Nucleotide Archive

Cochrane, G., Alako B., Amid C., Bower L., Cerdeno-Tárraga A., Cleland I., Gibson R., Goodgame N., Jang M., Kay S., et al.

Nucleic Acids Res. Volume 41, Number D1, (2013), p.D30-5 doi:

A decadal view of biodiversity informatics: challenges and priorities

A., Hardisty, D. Roberts, and Biodiversity Informatics Community

BMC Ecology. Volume 13, (2013), doi:

2012

The Sequence Read Archive: explosive growth of sequencing data

Kodama, Y., Shumway M., Leinonen R., and International Nucleotide Sequence Database Collaboration

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D54-6 doi:

The International Nucleotide Sequence Database Collaboration

Karsch-mizrachi, I., Nakamura Y., Cochrane G., and Collaboration International Nucleotide Sequence Database

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D33-7 doi:

The future of sequence archiving

Cochrane, G., Cook C. E., and Birney E.

GigaScience. Volume 1, (2012), doi:

Major submissions tool developments at the European Nucleotide Archive

Amid, C., Birney E., Bower L., Cerdeno-Tárraga A., Cheng Y., Cleland I., Faruque N., Gibson R., Goodgame N., Hunter C., et al.

Nucleic Acids Res. Volume 40, Number Database issue, (2012), p.D43-7 doi:

2011

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Yilmaz, P., Kottmann R., Field D., Knight R., Cole J. R., Amaral-Zettler L., Gilbert J. A., KARSCH-MIZRACHI I., Johnston A., Cochrane G., et al.

Nat Biotechnol. Volume 29, Number 5, (2011), p.415-20 doi:

The genomic standards consortium: bringing standards to life for microbial ecology

Yilmaz, P., Gilbert J. A., Knight R., Amaral-Zettler L., KARSCH-MIZRACHI I., Cochrane G., NAKAMURA Y., Sansone S. A., Glockner F. O., and Field D.

ISME J. Volume 5, Number 10, (2011), p.1565-7 doi:

The Sequence Read Archive

Leinonen, R., Sugawara H., Shumway M., and C Int Nucleotide Sequence Database

Nucleic Acids Research. Volume 39, (2011), p.D19-D21 doi:

The European Nucleotide Archive

Leinonen, R., Akhtar R., Birney E., Bower L., CERDENO-TARRAGA A., Cheng Y., Cleland I., Faruque N., Goodgame N., Gibson R., et al.

Nucleic Acids Res. Volume 39, Number Database issue, (2011), p.D28-31 doi:

2008

The minimum information about a genome sequence (MIGS) specification

Field, D., Garrity G., Gray T., Morrison N., Selengut J., Sterk P., Tatusova T., Thomson N., Allen M. J., Angiuoli S. V., et al.

Nat Biotechnol. Volume 26, Number 5, (2008), p.541-7 doi:

2007

EMBL nucleotide sequence database in 2006

Kulikova, T., Akhtar R., Aldebert P., Althorpe N., Andersson M., Baldwin A., Bates K., Bhattacharyya S., Bower L., Browne P., et al.

Nucleic acids research. Volume 35, Number suppl 1, (2007), p.D16–D20

2006

EMBL nucleotide sequence database: developments in 2005

Cochrane, G., Aldebert P., Althorpe N., Andersson M., Baker W., Baldwin A., Bates K., Bhattacharyya S., Browne P., van den Broek A., et al.

Nucleic acids research. Volume 34, Number suppl 1, (2006), p.D10–D15

2005

The EMBL nucleotide sequence database

Kanz, C., Aldebert P., Althorpe N., Baker W., Baldwin A., Bates K., Browne P., van den Broek A., CASTRO M., Cochrane G., et al.

Nucleic Acids Research. Volume 33, Number suppl 1, (2005), p.D29–D33

2004

The EMBL nucleotide sequence database

Kulikova, T., Aldebert P., Althorpe N., Baker W., Bates K., Browne P., van den Broek A., Cochrane G., Duggan K., EBERHARDT R., et al.

Nucleic Acids Research. Volume 32, Number suppl 1, (2004), p.D27–D30

2003

The EMBL nucleotide sequence database: major new developments

Stoesser, G., Baker W., van den Broek A., Garcia-Pastor M., Kanz C., Kulikova T., Leinonen R., LIN Q., Lombard V., Lopez R., et al.

Nucleic Acids Research. Volume 31, Number 1, (2003), p.17–22

2002

The EMBL nucleotide sequence database

Stoesser, G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Leinonen R., LIN Q., Lombard V., et al.

Nucleic acids research. Volume 30, Number 1, (2002), p.21–26

2001

The EMBL nucleotide sequence database

Stoesser, G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Lombard V., Lopez R., Parkinson H., et al.

Nucleic Acids Research. Volume 29, Number 1, (2001), p.17–21

1999

The EMBL nucleotide sequence database

Stoesser, G., Tuli M. A., Lopez R., and Sterk P.

Nucleic Acids Research. Volume 27, Number 1, (1999), p.18–24

Services

ENA

Metagenomics

Team members

Ana Cerdeño-Tárraga

Nima Pakseresht

Swapna Pallreddy

Sheila Plaister

Rajesh Radhakrishnan

Stephane Riviere

Nicole Silvester

Dmitriy Smirnov

Petra Ten Hoopen